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MicroBio > Exam 3 > Flashcards

Exam 3 Flashcards

1
Q

Genome

A

All the DNA present in a cell or virus

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2
Q

Genotype

A

specific set of genes an organisms possesses

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3
Q

Major targets for antibiotics

A
  1. cell wall
  2. protein synthesis
  3. DNA/RNA replication
  4. tetrahydrofolic acid biosynthesis
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4
Q

Phenotype

A

collection of observable characteristics

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5
Q

Fred Griffith was able to observe what phenomenon?

A

transformation

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6
Q

Nucleoside

A

nitrogenous base & 5 C sugar

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7
Q

Nucleotide

A

nucleoside-phosphate

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8
Q

360 turn of the helix = ____ bases

A

10

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9
Q

Most RNA molecules are ____ stranded

A

single stranded

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10
Q

Double stranded RNA can be found in

A

viral genomes

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11
Q

Small regulatory RNA (sRNA)

A
  • any RNA that is not making proteins
  • not translated
  • functional as RNA molecules
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12
Q

DNA replication is

A

semi-conservative

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13
Q

DNA polymerase

A

synthesizes complementary strand of DNA

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14
Q

T / F : DNA synthesis occurs only in one direction

A

T

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15
Q

New bases are only added to the ___ end of a DNA molecule

A

3’

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16
Q

What does DNA polymerase require?

A
  • template
    -primer
  • dNTPs
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17
Q

Template

A

directs synthesis of complementary strand

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18
Q

Primer

A

DNA or RNA strand

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19
Q

dNTPS

A

dATP, dTTP, dCTP, dGTP

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20
Q

Helicases

A

unwind DNA strands

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21
Q

Single stranded binding proteins (SSB)

A

keeps strands apart for replication to occur

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22
Q

DNA gyrase / topoisomerases

A

alter DNA supercoiling to relieve tension from rapid unwinding of double helix

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23
Q

Ligase

A

enzyme that attaches two pieces of single stranded DNA together

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24
Q

Leading strand is synthesized

A

continuously

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25
Q

Primase

A

synthesizes short complementary strands of RNA (~10 nucleotides) to serve as primers needed by DNA polymerase

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26
Q

Okazaki fragments

A

the short fragments of the lagging strand

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27
Q

DNA polymerase I

A

removes and replaces RNA primer with DNA

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28
Q

DNA ligase

A

forms a bond between 3’-hydroxyl of the growing strand and the 5’-phosphate of an Okazaki fragment

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29
Q

Exonuclease activity goes in what direction?

A

3’ to 5’

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30
Q

Catenates

A

form when the two circular daughter chromosomes do not separate

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31
Q

Okazaki fragments hinder

A

replication of ends of chromosomes

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32
Q

Coding strand

A

top strand

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33
Q

Template strand

A
  • bottom strand
  • read in 3’ to 5’ direction
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34
Q

Promoter is located ____ of the gene

A

upstream

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35
Q

Leader sequence is also known as

A

5’ untranslated region (5’ UTR)

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36
Q

Shine-Dalgarno

A
  • ribosome binding site
    -located within 5’ UTR
  • typically 6-10 nucleotides upstream of start codon
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37
Q

N-formylmehtionine

A

a modified amino acid used to initiate protein synthesis in bacteria

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38
Q

Stop codons

A

TAG, TAA, TGA, where coding region stops/translation stop site

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39
Q

T / F : no introns/exons in bacterial genes

A

T

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40
Q

Monocistronic

A
  • encodes for one gene
  • one gene = one protein
  • eukaryotes
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41
Q

Polycistronic

A
  • bacteria
  • directions for >1 polypeptide contained within one mRNA molecule
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42
Q

2 subunits of RNA polymerase

A

core enzyme and sigma factor

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43
Q

Holoenzyme

A

core enzyme + sigma factor

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44
Q

Transcription is carried out by

A

RNA polymerase

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45
Q

Promoter

A

site where RNA polymerase binds to initiate transcription
- site that sigma factor binds to

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46
Q

T / F : transcription termination is at stop codons

A

F

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47
Q

Describe how Rho-independent transcription termination works

A
  • no proteins involved
  • DNA sequence alone results in termination
  • RNA forms stem loop structure
  • knocks RNA polymerase off the DNA
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48
Q

Describe how Rho-dependent transcription termination works

A
  • Rho binds to mRNA at the rut site
  • moves along mRNA in direction of RNA polymerase
  • RNA polymerase pauses at Rho terminator
  • Rho catches up and knocks RNA polymerase off
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49
Q

Final step in expression of protein encoding genes is

A

translation

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50
Q

T / F : double strands are not always antiparallel

A

F

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51
Q

Start codon

A
  • start site for translation
  • typically AUG
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52
Q

Sense codons

A

61 codons that specify amino acids

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53
Q

Code degeneracy

A

up to six different codons can code for the same amino acid

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54
Q

Codons UAA and UAG can code for

A
  • stop
  • amino acids
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55
Q

How many naturally occurring amino acids are there?

A

20

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56
Q

Rare amino acids encoded by some microbes

A

Selenocysteine (Sec, U, UGA), Pyrrolysine (Pyl, O, UAG)

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57
Q

If GUG and UUG are first

A

they are start codons and encode f-Met

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58
Q

N terminus

A

like 5’ end

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59
Q

C terminus

A

like 3’ end

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60
Q

Polyribosome

A

complex of mRNA with several ribosomes attached to it

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61
Q

T / F : transcription and translation cannot be coupled in bacteria and archaea

A

F

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62
Q

tRNA has terminal ____ sequence

A

CCA

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63
Q

Charged tRNA

A

tRNA with amino acid attached

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64
Q

tRNA without amino acid

A

uncharged

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65
Q

Aminoacyl-tRNA synthetases

A

catalyzes attachment of amino acid to tRNA

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66
Q

rRNA

A
  • contributes to structure of ribosome
  • 16S rRNA
  • 23S rRNA
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67
Q

16S rRNA

A
  • binds to Shine Dalgarno site on mRNA for protein synthesis initiation
  • binds initiation factor 3 (protein needed for translation initiation) and 3’ end of charged tRNA
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68
Q

23S rRNA

A

ribozyme catalyzes peptide bond formation

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69
Q

What is usually removed after protein synthesis?

A

N-formylmethionine

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70
Q

Core enzyme

A

composed of 5 proteins and catalyzes RNA synthesis

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71
Q

Sigma Factor

A

has no catalytic activity but helps the core enzyme recognize the DNA at start of genes (promoter)

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72
Q

Transcription termination

A

occurs when core RNA polymerase dissociates from template DNA
- site where RNA synthesis ends

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73
Q

Translation

A

synthesis of polypeptide directed by sequence of nucleotides in mRNA (5’ to 3’)

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74
Q

Polyribosome

A

complex of mRNA with several ribosomes

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75
Q

Site of translation

A

ribosome

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76
Q

Two approaches to regulation

A
  • regulation of gene expression
  • alter activity of enzymes and proteins
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77
Q

Constitutive genes

A

housekeeping genes that are continuously expressed by the cell

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78
Q

Inducible genes

A
  • genes that are typically off but can be switched on
  • function in catabolic pathways
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79
Q

Repressible genes

A
  • genes that are typically on but can be shut off
  • repressible enzymes function in anabolic pathways
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80
Q

T / F: inducible enzymes are present only when their substrate is available

A

T

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81
Q

Inducer

A

effector molecule

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82
Q

Beta galactosidase hydrolyses ____ into ___ and ____

A

lactose, galactose and glucose

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83
Q

Beta galactosidase gene is only “on” when ____ is available

A

lactose

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84
Q

Typically, enzymes that function in biosynthetic pathways are products of

A

repressible genes

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85
Q

Induction and repression occur because of the activity of ____ containing ____

A

regulatory proteins, DNA binding domains

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86
Q

Regulatory proteins bind to DNA and can do one of what two things?

A

inhibit transcription or promote transcription

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87
Q

Repressors

A

inhibit transcription

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88
Q

Activators

A

promote transcription

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89
Q

Negative transcriptional control (overview and result)

A
  • binding of regulatory protein (repressor) at DNA regulatory site (operator) inhibits initiation of transcription
  • mRNA expression is reduced
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90
Q

_____ or _____ alter activity of repressor

A

inducers, corepressors

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91
Q

Positive control (overview and result)

A
  • binding of a regulatory protein (activator) at a regulatory region on DNA (activator binding sites) promotes transcription initiation
  • mRNA synthesis is increased
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92
Q

Inactive protein is activated by

A

inducer

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93
Q

Active protein is inactivated by

A

inhibitor

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94
Q

T / F: enzymes of a catabolic pathway are not only needed when the preferred substrate is available

A

F

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95
Q

3 structural genes coding for lactose uptake and metabolism

A

lacZ, lacY, lacA

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96
Q

Control of Lac operon is (+) or (-) ?

A

has negative and positive control

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97
Q

Expression of Lac operon is repressed by

A

Lacl repressor

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98
Q

____ of Lacl form and bind to three operator sites

A

tetramers

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99
Q

Allolactose binds ____

A

Lacl repressor

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100
Q

Catabolite activator protein

A
  • regulates lac operon in response to presence or absence of glucose
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101
Q

When ___ is present, lac operon will not be activated

A

glucose

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102
Q

When ____ is absent, lac operon will be activated

A

glucose

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103
Q

Tryptophan operon consists of how many structural genes?

A

5

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104
Q

Trp operon only functions in the absence of ____

A

tryptophan

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105
Q

Attenuation

A

termination of transcription within the leader region

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106
Q

Trp experiences what type of regulation of transcription elongation?

A

attenuation

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107
Q

T/ F: transcription (attenuation) terminates after the gene is transcribed

A

F

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108
Q

Attenuation of the trp operon

A
  • the trp leader sequence contains a short peptide called TrpL
  • during transcription, the trp mRNA leader sequence forms secondary structure
  • 2 hairpin loops form (regions 1 and 2, regions 3 and 4)
  • regions 3 and 4 form transcription terminator
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109
Q

T/F: in attenuation of the trp operon, transcription and translation are coupled

A

T

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110
Q

TrpL has ___ Trp codons

A

2

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111
Q

What happens if amount of charged Trp tRNA is low?

A

ribosome stalls at region 1

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112
Q

Where does the anti-terminator form when there is a low amount of charged Trp tRNA?

A

2 and 3

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113
Q

What happens if amount of charged Trp tRNA is high?

A

ribosome does not stall at region 1

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114
Q

Where does the anti-terminator form when there is a high amount of charged Trp tRNA?

A

3 and 4

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115
Q

Riboswitches

A

a specialized form of transcription attenuation

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116
Q

Folding of ___ also known as _____ determines if transcription will continue/terminate

A

leader sequence, the riboswitch

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117
Q

Folding pattern altered in response to mRNA binding of a(n)

A

effector molecule

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118
Q

T / F: cis-acting regulatory elements are part of the same RNA transcript they regulate

A

T

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119
Q

Small RNAs (sRNAs)

A
  • typically are complementary (antisense) to mRNA and function by base pairing
  • may inhibit or enhance translation
  • trans-acting RNAs
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120
Q

T/ F: sRNAs function as mRNA, tRNA, or rRNA

A

F

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121
Q

Why are global regulators important for bacteria?

A

because they must respond rapidly to wide variety of changing conditions

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122
Q

Regulon

A

set of genes or operons controlled by a common regulatory protein

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123
Q

Types of regulation global regulatory systems use

A
  • regulatory proteins
  • alternative sigma factors
  • phosphorelay systems
  • two component signal transduction systems
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124
Q

Many genes and operons are turned on or off in response to ____

A

environmental conditions

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125
Q

Common system used by bacteria to regulate gene expression in response to environmental conditions are _____

A

two-component signal transduction systems (TCSTS)

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126
Q

T / F: two component regulatory system is found in all three domains of life

A

T

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127
Q

Two proteins of the two component regulatory system

A

sensor kinase and response-regulatory protein

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128
Q

Sensor kinase (histidine kinase)

A
  • extracellular receptor for sensing
  • intracellular communication domain
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129
Q

Response-regulatory protein

A
  • intracellular protein
  • activated by sensor kinase
  • DNA binding protein
    ^ activator, repressor
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130
Q

Activation of sensor kinase results in

A

phosphorylation of histidine

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131
Q

In RRP, phosphate group is transferred from ___ to ___

A

His (H), Asp (D)

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132
Q

EnvZ

A

phosphorylated in high osmolarity

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133
Q

OmpR

A

phosphorylated and regulates transcription

134
Q

The OmpR/EnvZ two component signal transduction system

A

regulates expression of outer membrane proteins (OmpC and OmpF) depending on osmolarity

135
Q

OmpC

A

makes smaller pore in membrane, lower levels of diffusion into the cell

136
Q

OmpF

A

makes larger pore in membrane, allows more diffusion of solutes

137
Q

High osmolarity leads to

A

autophosphorylation of EnvZ —> –> –> OmpR activates OmpC

138
Q

Low osmolarity leads to

A

no phosphorylation of EnvZ, no activation of OmpC

139
Q

T / F: machinery involved in replicating and expressing archaeal genomes is more like that of eukaryotes than that of bacteria

A

T

140
Q

DNA polymerase catalyzes synthesis of

A

complementary strand of DNA

141
Q

Template

A

directs synthesis of complementary strand

142
Q

Primer

A

DNA or RNA strand

143
Q

dNTPs

A

dATP, dTTP, dCTP, dGTP

144
Q

Eukaryotic chromosomes are ____ while bacterial are ___

A

linear, circular

145
Q

Polymerase enzymes require

A
  • template
  • primer
  • dNTPs
146
Q

Bacterial chromosome is ___ Mb

A

2.5

147
Q

Eukaryotic chromosomes are wound around

A

histone proteins

148
Q

3 DNA polymerases responsible for eukaryotic DNA replication

A
  • α-primase
  • Pol ε
  • Pol δ
149
Q

Pol δ

A

appears to synthesize the lagging strand

150
Q

Pol ε

A

appears to synthesize the leading strand

151
Q

α-primase

A

lays down an RNA/DNA hybrid starting point

152
Q

Chromosome ends may be digested by

A

DNAses

153
Q

What are some challenges presented by linear DNA molecules?

A
  • chromosome ends may be digested
  • DNA ends can fuse with other DNA molecules
  • the “end replication problem”
154
Q

Telomerase

A

ribonucleoprotein complex enzyme that forms the telomeres and maintains them

155
Q

Telomerase has an internal _______ that partially matches the _______

A

RNA template, G-tail sequence

156
Q

Telomerase uses the _____ of the G tail as a DNA synthesis starting point

A

3’ OH

157
Q

The internal RNA sequence is used as the template for

A

DNA synthesis

158
Q

The _______ activity of telomerase increases the length of the G-tail

A

reverse transcriptase

159
Q

Lengthening the G-tail creates enough room to make a(n) ____ on the _____

A

RNA primer, lagging strand

160
Q

T / F: archaeal chromosomes are more similar to eukaryotes than bacteria

A

F

161
Q

T / F: some archaea have histones associated with their chromosomes

A

T

162
Q

Archaeal chromosomes, like bacterial, are ___

A

circular

163
Q

Archaeal and bacterial chromosomes are similar in ____ and ___

A

size, structure (circular)

164
Q

Most archaea have how many origin of replication?

A

one

165
Q

_________ in archaea are similar to those of eukaryotes

A

replisome proteins

166
Q

___ family use the same family of DNS polymerases as eukaryotes

A

B

167
Q

T / F: on a molecular level, transcription is very similar in all organisms

A

T

168
Q

What direction is RNA produced in?

A

5’ to 3’

169
Q

Promoter is located at the ____

A

start of the gene

170
Q

Two characteristics of a promoter

A
  • recognition/binding site for RNA polymerase
  • orients polymerase
171
Q

The bacterial RNA polymerase is known as

A

holoenzyme

172
Q

Holoenzyme is composed of

A

sigma factor, core enzyme

173
Q

Sigma factor

A

has no catalytic activity but helps the core enzyme recognize the start of genes

174
Q

How many polymerase do bacteria have for transcription?

A

1, have multiple sigma factors

175
Q

Where does eukaryotic transcription occur?

A

nucleus

176
Q

Exons

A

regions coding for protein that end up in the mRNA

177
Q

Introns

A

code for RNA that is never translated into protein

178
Q

T / F: most eukaryotes have singlet protein-coding genes (monocistronic transcripts)

A

T

179
Q

3 major types of RNA polymerase

A

RNA pol II
RNA pol I
RNA pol III

180
Q

RNA polymerase II catalyzes

A

mRNA synthesis

181
Q

RNA polymerase I catalyzes

A

rRNA synthesis

182
Q

RNA polymerase III catalyzes

A

tRNA synthesis

183
Q

T / F: promoters do not differ between eukaryotes and bacteria

A

F

184
Q

Elements that define the core promoter

A
  • TATA box
  • BRE (TFIB recognition element)
  • Inr (initiator element)
  • DPE (downstream promoter element)
185
Q

T / F: eukaryotic and archaeal promoters share sequences

A

T

186
Q

T / F: no sigma factor in eukaryotes or archaea

A

T

187
Q

Eukaryotes and archaea use _____ instead of sigma factors

A

transcription factors

188
Q

Transcription factors

A

bind to DNA and line the polymerase up to it correctly

189
Q

How must initial transcripts be modified before they are ready to be translated?

A
  • 5’ cap of 7-methylguanosine added
  • removal of introns/splicing together exons
  • addition of 3’ poly a tail
190
Q

Spliceosome

A

large complex of proteins and RNA molecules unique to eukaryotes, removes introns

191
Q

Alternative splicing

A

different ways of joining exons together

192
Q

T / F: alternative splicing can be found in any domain

A

F, only in eukaryotes

193
Q

What mechanism allows for a smaller number of genes to code for a greater number of products in cells?

A

alternative splicing

194
Q

Similarities between archaeal transcription and eukaryotic

A
  • RNA polymerase resembles polymerase II
  • archaeal promoters and binding of the RNA polymerase
  • no sigma factors
195
Q

Similarities between archaeal transcription and bacterial

A
  • transcription occurs in the cytoplasm
  • coupling of transcription/translation
  • mRNA is polycistronic
  • introns are rare
196
Q

Introns in archaea and bacteria are thought to be excised by

A

different methods, maybe something like tRNA splicing in eukaryotes

197
Q

Eukaryotic translation requires more or less initiation factors for proper positioning on the mRNA?

A

more

198
Q

Eukaryotic ribosome size:
Bacterial ribosome size:

A

80S
70S

199
Q

Eukaryotic initiation factors bind to

A

the 5’ cap

200
Q

PABPs bind to

A

3’ poly-A tail

201
Q

The cap/tail protein complexes form a _____, activating the _____

A

bridge, mRNA molecule

202
Q

Initiator tRNA (Met) interacts with ____ to form ____

A

40S ribosomal subunit, 43S subunit

203
Q

43S binds to the activated ______

A

(bridged) mRNA

204
Q

____ is recruited after _____ to begin elongation steps

A

60S, 43S unit scans the mRNA for start codon

205
Q

T / F: elongation and termination are similar in eukaryotes and bacteria

A

T

206
Q

Polysomes

A

observed in eukarya, more than one ribosome translating the same mRNA molecule

207
Q

T / F: no N-formylmethionine in archaeal translation

A

T

208
Q

Transcription and translation are ____ in archaea

A

coupled

209
Q

Polycistronic transcripts

A

each coding region translated into separate protein

210
Q

Regulation of cellular processes can take place at what 3 levels

A

transcriptional, translational, posttranslational

211
Q

Activator binding sites include

A

upstream activating sequences, and enhancers

212
Q

Upstream activating sequences (UASs)

A

near the promoter of the gene regulated

213
Q

Enhancers

A
  • either upstream or downstream of the promoter
  • exert effects from a distance
214
Q

Repressor binding sites

A

silencers

215
Q

Histones act as a _____ in transcription

A

road block

216
Q

Acetylation of histones _____ transcription

A

promotes

217
Q

Methylation of histones _____ transcription

A

represses

218
Q

T / F: histone acetylation is a gene regulation/control mechanism unique to eukaryotes

A

T

219
Q

Examples of regulatory mechanisms for gene expression

A

antisense RNAs that function at the translation level, riboswitches, sRNA molecules

220
Q

Riboswitches

A
  • in bacteria: transcription elongation/translation
  • control whether or not RNA splicing occurs
221
Q

sRNA molecules

A

regulate gene expression via alternative splicing modulation

222
Q

Other RNA based regulatory mechanisms in eukaryotes

A
  • micro RNAs (miRNAs)
  • small interfering RNAs (siRNAs)
223
Q

siRNAs

A
  • form complexes with proteins including argonaute (AGO)
  • function at translational level
  • prevent translation initiation and elongation
  • can also degrade mRNAs
224
Q

Levels of gene regulation

A
  • transcription initiation
  • splicing efficiency
  • mRNA trafficking
  • mRNA stability/degradation
  • translational rate
  • post-translational modification
225
Q

T / F: regulation of transcription initiation in archaea has similar machinery to eukaryotes

A

T

226
Q

Mutations

A

stable, heritable changes in sequence of bases in DNA

227
Q

Most common kind of mutation:

A

point

228
Q

Point mutations

A
  • single nucleotide polymorphism, single nucleotide is changed (A to G)
  • insertion or deletion (AAAA to AAA or AAA to AAAA)
229
Q

consequence of mutation depends on ___ and ___

A

type and location

230
Q

If a mutation occurs within a gene, it is called a(n)

A

coding DNA sequence, CDS, mutation

231
Q

If a mutation is between two genes, it is called a(n)

A

intergenic (IG) mutation

232
Q

An SNP CDS mutation would result in what?

A

a silent mutation, no amino acid change OR missense, amino acid change

233
Q

An SNP IG mutation would result in what?

A
  • no effect
  • alter gene expression
  • sRNAs
234
Q

An Indel CDS mutation would result in what?

A

a frameshift, multiple amino acid changes/stop codon

235
Q

An Indel IG mutation would result in what?

A
  • no effect
  • alter gene expression
  • sRNAs
236
Q

Consequences of mutations manifest as

A

phenotypic changes

237
Q

What are consequences of a change in protein sequence?

A
  • loss of function
  • gain of function
238
Q

Error rate of DNA polymerase

A

10E-9 errors per base

239
Q

Errors per genome replication (bacteria)

A

5Mbp

240
Q

Mismatch repair

A
  • type of excision repair
  • mismatch correction enzyme (MutS) scans newly synthesized DNA for mismatched pairs
  • mismatched pairs removed and replaced by DNA pol and DNA ligase
  • repair system uses methylation to “know” which strand is correct
241
Q

DNA methylation

A

used by E. coli mismatch repair system to distinguish old DNA strands from new DNA strands

242
Q

The E. coli mismatch repair system cuts out the mismatch from the ____ strand

A

unmethylated

243
Q

Vertical gene transfer

A

transfer of genes from parents to progeny

244
Q

Genetic variation in VGT is primarily due to

A
  • fusion of male and female gametes
  • crossing over between sister chromatids during meiosis
245
Q

Source of genetic variability for eukaryotes

A

sexual reproduction

246
Q

Genetic variability (in prokaryotes) primarily due to

A

horizontal gene transfer

247
Q

HGT differs from VGT in what ways?

A
  • transfer of genes from one independent, mature organism to another
  • genes can be transferred to the same or different species
  • if transfer is stable, recipient acquires function of transferred gene
248
Q

What does it mean for DNA to be stable?

A

self replicating, able to be integrated onto chromosome

249
Q

Integrating into the host genome occurs by

A

recombination

250
Q

2 major types of recombination

A

homologous recombination, site specific recombination

251
Q

What is the most common type of recombination?

A

homologous

252
Q

Homologous recombination

A
  • occurs between two long sequences of DNA with same/similar sequence
  • double-strand break occurs
  • adjacent molecules are rejoined to each other
  • involves the RecA protein
253
Q

Site-specific recombination is important in

A

insertion of viral genome into host chromosomes and transposons

254
Q

3 important differences between site-specific recombination and homologous

A
  • does not require long regions of DNA homology
  • recombination occurs at specific target sites in DNA molecules
  • mediated by specific enzymes called recombinases
255
Q

2 major types of transmissible DNA

A
  • transposable elements
  • plasmids
256
Q

3 mechanisms for HGT

A
  • conjugation
  • transformation
  • transduction
257
Q

Transposition

A

process by which small segments of DNA move about the genome

258
Q

Insertion sequences

A

simplest transposable elements

259
Q

Composite transposons (Tn)

A

transposable elements which contain “extra” genes, flanked by two IS

260
Q

Unit transposons are between ___ and ___

A

IS, composite Tn

261
Q

Unit transposons

A

like expanded IS but can contain “extra” genes

262
Q

Inverted repeats

A
  • short stretch of identical nucleotides in opposite orientation
  • marks the ends of the IS/Tn
263
Q

Transposase

A

enzyme responsible for site specific transposition

264
Q

Direct repeats

A
  • host DNA that is the site for insertion
  • duplicated during insertion
265
Q

2 mechanisms of action for transposition

A
  1. simple transposition (cut and paste)
  2. replicative transposition (copy and paste)
266
Q

Simple transposition

A
  • cut and paste
  • transposase catalyzes excision of TE
  • TE is bound by transposase and migrates to new insertion site
  • new target site is cleaved and TE ligated into site
  • target site is replicated in the process (DR)
267
Q

Replicative transposition

A
  • original transposon remains at parental site in DNA
  • copy is inserted in target DNA
  • retrotransposons
268
Q

Plasmids

A
  • small, extrachromosomal circular DNA molecules
  • exist and replicate independently of chromosome
  • contain non essential genes
269
Q

Episomes

A

can integrate reversibly into the host chromosome

270
Q

Conjugative plasmids

A

can transfer copies of themselves to other bacteria during conjugation

271
Q

Retrotransposons

A
  • RNA copy of TE is made
  • reverse transcribed into DNA
  • integrates at new site
272
Q

Plasmid is replicated by

A

rolling circle method

273
Q

F factor codes for

A

sex pilus and all machinery needed for plasmid transfer

274
Q

F plasmid is an

A

episome

275
Q

Integration of F plasmid occurs at

A

insertion sequences

276
Q

When F factor is not integrated into chromosome, cell is called ____

A

F+

277
Q

When F factor is integrated into chromosome, cell is called ____

A

HFr

278
Q

T / F: conjugation cannot occur between HFr and F- strains

A

F

279
Q

F’ plasmid forms when

A

the F factor incorrectly excises from the host chromosome

280
Q

T / F: in F’ conjugation, some of the F factor is left behind in the host chromosome and/or some host genes have been removed along with some of the F factor

A

T

281
Q

Transformation

A

uptake of extracellular DNA by a bacterial cell

282
Q

Competent cells

A

bacterial cells that have the ability to take up DNA

283
Q

Competent cells are ____ when they take up DNA

A

transformed

284
Q

DNA being transformed may be ___ or ___

A

circular (plasmid) or linear (fragment of genomic DNA)

285
Q

For linear DNA to be stably transformed, it must

A

integrate into the chromosome

286
Q

Transduction

A

the transfer of bacterial genes by viruses

287
Q

Lytic

A

host cell is destroyed

288
Q

Lysogenic

A

viral DNA integrates into the host genome (becoming prophage)

289
Q

Two potential cycles of transduction

A

lytic and lysogenic

290
Q

Phage mediated transduction

A
  • host genes transferred by bacteriophage
  • typically an “accidental” process
  • results from errors in phage life cycle
291
Q

2 types of phage mediated transduction

A
  • generalized transduction
  • specialized transduction
292
Q

Generalized transduction

A
  • occurs because of errors in lytic cycle
  • any part of bacterial genome can be transferred
  • during viral assembly, fragments of host DNA mistakenly packaged into phage head
293
Q

Specialized transduction

A
  • occurs because of errors in lysogenic cycle
  • occurs when prophage is incorrectly excised
  • new virions contain part of the viral genome plus host DNA surrounding viral integration site
  • host DNA is introduced into recipient cell
  • can recombine into genome or integrate with partial phage genome
  • host DNA transferred is that surrounding viral integration site
294
Q

Generalized transducing particles

A
  • bacterial DNA wrapped in viral proteins
  • no viral DNA
  • can be easily transferred to another bacterial cell
295
Q

Phage lambda specialized transduction

A

recipient becomes gal+

296
Q

Mechanisms of drug resistance

A
  • modification of target enzyme or organelle
  • inactivation of drug
  • efflux pumps
  • use of alternative pathways or proteins
297
Q

How does antibiotic resistance occur?

A
  • mutations (arise spontaneously and are then selected for)
  • horizontal gene transfer of resistance genes
298
Q

Resistance genes can be found on

A
  • bacterial chromosomes
  • plasmids
  • transposons
299
Q

Genetic engineering

A

deliberate modification of organism’s genetic information by directly changing the sequence of nucleic acids in its genome

300
Q

Recombinant DNA

A

artificially created DNA sequences, results from combining 2 strands of DNA together

301
Q

Cloning

A

generating a large number of genetically identical DNA molecules

302
Q

Biotechnology

A

use of biological organisms to form useful products

303
Q

Industrial microbiology

A

use of microbes to manufacture important compounds

304
Q

What are the 2 main reasons you might want to express a foreign gene in a host cell?

A
  • to determine its function
  • to purify the protein
305
Q

Recombinant DNA technologies

A
  • restriction enzymes
  • genetic cloning
  • PCR
    -DNA sequencing
306
Q

Restriction enzymes (RE)

A
  • recognize and bind specific sequences in DNA called recognition sites
307
Q

Type II RE cleave

A

DNA at/around the site

308
Q

Type I and III cleave

A

a defined distance from this site

309
Q

Cleavage with restriction enzymes may produce

A

blunt or sticky ends

310
Q

Palindromes

A

same going forward as it is going backwards

311
Q

Vectors

A

carriers of foreign DNA

312
Q

4 types of cloning vectors

A
  • phages and viruses
  • cosmids
  • artificial chromosomes
  • plasmids (most commonly used)
313
Q

Cloning a gene

A
  • foreign DNA combined with/inserted into a cloning vector
  • newly created plasmid is a recombinant DNA molecule
  • inside a new host cell plasmid vector replicates
  • maintains foreign DNA fragment (gene)
314
Q

Characteristics of good cloning vectors

A
  • replicate autonomously
  • easy to purify
315
Q

Requirements for vectors

A
  • origin of replication
  • selectable marker (ex: antibiotic resistance gene)
316
Q

Multiple cloning site (MCS)

A
  • site where cloned gene to be inserted into the plasmid vector
  • contains many unique RE sites
  • may contain selection gene
317
Q

PCR

A

technique that enables DNA amplification

318
Q

Specificity of PCR arises from

A

DNA primers

319
Q

Oligonucleotides

A

short DNA molecules that flank the DNA sequence being amplified, serve as primers for DNA polymerase

320
Q

PCR cycle

A
  • DNA is denatured
  • primers anneal to target DNA
  • target DNA is synthesized (amplified)
  • repeat 34x
321
Q

PCR reaction mix contains:

A
  • primers
  • template DNA (target)
  • thermostable DNA polymerase (taq)
  • dNTPs (dATP, dCTP, dTTP, dGTP)
322
Q

Number of copies of DNA produced in PCR reaction =

A

2^n, where n = how many cycles were done

323
Q

Uses of PCR

A
  • simplifies gene cloning
  • generates DNA fragments
  • may amplify environmental genes without culturing the microbes
  • diagnostic purposes
324
Q

Limitations of PCR

A
  • mutations due to Taq polymerase
  • cannot have a completely unknown sample
325
Q

Most common method for determining DNA sequences

A

Sanger DNA sequencing

326
Q

How does Sanger sequencing work?

A

referred to as the chain-termination DNA sequencing method, uses dideoxynucleoside triphosphates (ddNTP), strand synthesis terminates when ddNTP is incorporated

327
Q

Sanger sequencing original method

A

newly synthesized DNA strands were labeled with radioactive atom, electrophoresed and detected with X ray film

328
Q

Sanger sequencing, modern method

A

automated sequencing, uses four different fluorescent color dyes instead of radio-labeled ddNTP, electrophoresis and laser beam determines order

329
Q

NGS (next generation DNA sequencing)

A

sequences millions of DNA strands simultaneously

330
Q

Sanger vs NGS (bp comparison)

A

Sanger: 1,000 bp/reaction
NGS: 10-100 billion bp/reaction

MicroBio (4 decks)

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